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Kenya is classified as one of the fastest growing countries in Africa. With this growth there has been increase in the application of Information and Communication Technology (ICT) in the major ministries in the government which includes the Ministry of Health. This has been in the areas of electronic medical records, technologies that assist in imaging such as MRI scans, immunizations, and appointments, among others. The Ministry of Health in Kenya uses many applications to capture data in the health facilities, which include IQCARRE and FUNSOFT. However, the reporting system used is DHIS which runs parallel to these systems hence forcing the health workers to re-enter the data for transmission to decision makers at Afya House. This causes redundancies in data entry, and increases reporting time which in turn delays necessary action by the key decision makers. A case study methodology was used to assess the decision making process in the Ministry of Health and also the activities involved in electronic data collection in Mbagathi and Kenyatta National Hospital. This was done through structured questionnaires. The results of the data analysis indicated that there was a disconnect between the data capture and reporting due to the use of different systems. The results also indicated that there was a need for a data mining based decision making system that could read the data in the data capture systems and transmit it to the decision makers. The prototype was developed and tested by both the health workers and the decision makers. From testing and responses from the health workers and decision makers, the prototype helped to standardize the reporting system and increased reporting time. The researcher recommended that the prototype be improved to cover all areas at the scope only covered patient and disease data.